To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("mzR")
In most cases, you don't need to download the package archive at all.
mzR
parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data)
Bioconductor version: 3.0
mzR provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a wrapper for the ISB random access parser for mass spectrometry mzXML, mzData and mzML files. The package contains the original code written by the ISB, and a subset of the proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.
Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou
Maintainer: Bernd Fischer <bernd.fischer at embl.de>, Steffen Neumann <sneumann at ipb-halle.de>, Laurent Gatto <lg390 at cam.ac.uk>, Qiang Kou <qkou at umail.iu.edu>
Citation (from within R,
enter citation("mzR")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("mzR")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("mzR")
| R Script | Accessin raw mass spectrometry and identification data | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DataImport, Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software |
| Version | 2.0.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) |
| License | Artistic-2.0 |
| Depends | Rcpp (>= 0.10.1), methods, utils |
| Imports | Biobase |
| LinkingTo | Rcpp |
| Suggests | msdata, RUnit, faahKO, mzID, BiocStyle, knitr, BiocGenerics |
| SystemRequirements | GNU make, NetCDF, zlib |
| Enhances | |
| URL | https://github.com/sneumann/mzR/ |
| Depends On Me | MSGFgui, MSnbase, TargetSearch, xcms |
| Imports Me | MSnID, Pbase, RMassBank |
| Suggests Me | qcmetrics, RforProteomics |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | mzR_2.0.0.tar.gz |
| Windows Binary | mzR_2.0.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | mzR_2.0.0.tgz |
| Mac OS X 10.9 (Mavericks) | mzR_2.0.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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